The UN security council has called for an impartial investigation into Israel's botched assault on a flotilla carrying aid supplies to the Gaza Strip, but it stopped short of an outright condemnation of the attack.

At least nine pro-Palestinian activists were killed in the raid yesterday as Israeli naval commandos stormed the Mavi Marmara, the largest ship in the flotilla carrying passengers. Dozens more were wounded, including at least one British man. The injured were taken to Israeli hospitals. It sparked a wave of global condemnation and protests.

Israel said more than 10 of its troops were injured, two seriously, in the battle that began early yesterday in international waters, about 40 miles from the Gaza coast. Israeli officials say about 50 of the 671 activists aboard the flotilla have been taken to Israel's international airport for deportation.

The flotilla was trying to break the Israeli blockade of Gaza, which has been enforced for the past three years.

Organisers of the flotilla said today they are sending two more ships to the area within the next few days. Greta Berlin of the Free Gaza Movement said a cargo boat is already on the way to challenge Israel's blockade of Gaza and a second boat carrying about three dozen passengers is expected to join it.

After a 10-hour emergency meeting that stretched into the earlier hours of today, the 15 council members agreed on a presidential statement that was weaker than that initially demanded by the Palestinians, Arabs and Turkey.

They had called for condemnation of the attack by Israeli forces "in the strongest terms" and "an independent international investigation".

But the statement said: "The security council deeply regrets the loss of life and injuries resulting from the use of force during the Israeli military operation in international waters against the convoy sailing to Gaza. The council, in this context, condemns those acts which resulted in the loss of at least 10 civilians and many wounded, and expresses its condolences to their families."

Last night Turkey, whose relations with Israel have been severely strained since the war in Gaza in 2008-09, called for Nato to convene over the military assault.

The Turkish prime minister, Recep Tayyip Erdogan, who ordered the recall of the country's ambassador to Israel, described the operation as "state terrorism" and said Israel had violated international law. "We are not going to remain silent in the face of this inhumane state terrorism," he said.

Israel immediately imposed a communications blackout on the detained activists – some were taken by bus to Be'er Sheva prison in the south of Israel – while simultaneously launching a sophisticated public relations operation to ensure its version of events was dominant. Its prime minister, Binyamin Netanyahu, who defended the assault, postponed today's meeting with Barack Obama at the White House to fly back to deal with the crisis.

Activists with less serious injuries began to trickle into Israeli hospitals late yesterday afternoon. There were believed to be about 27 British civilians aboard the flotilla, and last night the Foreign Office confirmed that at least one had been injured. Most of the dead were reported to be Turkish nationals.

The deaths and injuries were condemned by the UN, EU and other countries. The US, in contrast, was restrained in its response, expressing regret and saying it was "currently working to understand the circumstances surrounding this tragedy".

The UN secretary general, Ban Ki-moon, condemned the violence and called for an investigation. "I am shocked by reports of killing of people in boats carrying supply to Gaza. I heard the ships were in international water. That is very bad," he said.

The prime minister, David Cameron, described the assault as "unacceptable". In a telephone conversation with Netanyahu last night, the prime minister insisted Britain remains committed to Israel's security, but called for a "constructive" response to "legitimate criticism" of its actions.

The foreign secretary, William Hague, issued a statement "deploring" the loss of life. "There is a clear need for Israel to act with restraint and in line with international obligations," he said.

The Palestinian president, Mahmoud Abbas, described the storming of the flotilla as a "massacre" and called for three days of national mourning. Israel's navy had promised to exercise restraint in dealing with the flotilla, and the bloodshed will inevitably leave Israel open to charges of a disproportionate response involving excessive force.

The Israeli government, however, defended its actions saying its troops had been provoked by activists aboard the Mavi Marmara.

However, some Israeli commentators expressed reservations about the operation, fearing it would leave Israel internationally isolated. Alon Liel, a former Israeli ambassador to Turkey, told the Guardian the situation could have been averted. "Definitely we made mistakes and in retrospect anything would have been better – including letting the boats reach Gaza," he said.

The assault began at 4.30am as the convoy was heading to Gaza to deliver its aid cargo. According to a spokeswoman for the Israeli defence force (IDF), Avital Leibovich, officers aboard its warships gave the activists several warnings before commandos were winched from helicopters on to the deck of the Mavi Marmara.

"We found ourselves in the middle of a lynching," she told reporters in the Israeli port of Ashdod. About 10 activists had attacked commandos, taking their pistols, she said. "It was a massive attack," she said. "What happened was a last resort."

It was impossible to contact protesters on the ships, but the Free Gaza Movement, one of the organisers of the flotilla, said the IDF had started the violence, firing as soon as troops boarded the ship.

The Free Gaza Movement said later that one of the ships in the flotilla, the Irish-owned MV Rachel Corrie, was not intercepted, as it had been behind the rest of the vessels following a delay. Carrying among others the Northern Irish Nobel peace laureate Máiread Corrigan-Maguire and Denis Halliday, the Irish former UN assistant secretary, it remained in international waters off Gaza, pending a decision as to where it would head next.

The Mavi Marmara was brought into port at Ashdod, 23 miles north of Gaza City, last night following the earlier arrival of two other passenger ships. The area was closed to the media.

Activists were expected to be processed in a large white tent on the quayside, where they would be offered the choice of immediate deportation to their country of origin or going through the lengthy process of the Israeli courts system.

The Israeli authorities gave no details of the injuries to activists, but confirmed that nine were dead, although government sources said the figure could rise.

Israel advised its nationals in Turkey to leave the country for fear of reprisals.

Israeli police cancelled leave and the army was on high alert, saying it feared possible rocket attacks from Islamist militants in Gaza and southern Lebanon. Last night a rocket fired from Gaza landed in Israel. No one was injured.